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diff --git a/cmake-build-release/.cmake/api/v1/reply/cmakeFiles-v1-79ef2550a7a9eed04fc3.json b/cmake-build-release/.cmake/api/v1/reply/cmakeFiles-v1-79ef2550a7a9eed04fc3.json
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- TARGET_COMPILE_PDB = opengl/CMakeFiles/OpenGLStuff.dir/OpenGLStuff.pdb
- TARGET_PDB = opengl/libOpenGLStuff.pdb
# =============================================================================
@@ -425,9 +441,8 @@ build opengl/libOpenGLStuff.a: CXX_STATIC_LIBRARY_LINKER__OpenGLStuff_Release op
OBJECT_DIR = opengl/CMakeFiles/OpenGLStuff.dir
POST_BUILD = :
PRE_LINK = :
- TARGET_COMPILE_PDB = opengl/CMakeFiles/OpenGLStuff.dir/OpenGLStuff.pdb
TARGET_FILE = opengl/libOpenGLStuff.a
- TARGET_PDB = opengl/libOpenGLStuff.pdb
+ TARGET_PDB = OpenGLStuff.a.dbg
# =============================================================================
# Object build statements for EXECUTABLE target opengl_example_run
@@ -444,8 +459,6 @@ build opengl/CMakeFiles/opengl_example_run.dir/opengl_visualization.cpp.o: CXX_C
INCLUDES = -I/Users/adamwahab/Desktop/project-in-bioinformatics/third_party/glm -I/Users/adamwahab/Desktop/project-in-bioinformatics/third_party/glad/include -I/Users/adamwahab/Desktop/project-in-bioinformatics/third_party/imgui -I/Users/adamwahab/Desktop/project-in-bioinformatics/third_party/imgui/backends -iframework /Library/Developer/CommandLineTools/SDKs/MacOSX13.3.sdk/System/Library/Frameworks -isystem /opt/homebrew/include
OBJECT_DIR = opengl/CMakeFiles/opengl_example_run.dir
OBJECT_FILE_DIR = opengl/CMakeFiles/opengl_example_run.dir
- TARGET_COMPILE_PDB = opengl/CMakeFiles/opengl_example_run.dir/
- TARGET_PDB = opengl/opengl_example_run.pdb
# =============================================================================
@@ -461,9 +474,8 @@ build opengl/opengl_example_run: CXX_EXECUTABLE_LINKER__opengl_example_run_Relea
OBJECT_DIR = opengl/CMakeFiles/opengl_example_run.dir
POST_BUILD = :
PRE_LINK = :
- TARGET_COMPILE_PDB = opengl/CMakeFiles/opengl_example_run.dir/
TARGET_FILE = opengl/opengl_example_run
- TARGET_PDB = opengl/opengl_example_run.pdb
+ TARGET_PDB = opengl_example_run.dbg
#############################################
@@ -563,8 +575,6 @@ build test/CMakeFiles/test_run.dir/basic_tests/basic_check.cpp.o: CXX_COMPILER__
INCLUDES = -I/Users/adamwahab/Desktop/project-in-bioinformatics/src -I/Users/adamwahab/Desktop/project-in-bioinformatics/src/fmt -isystem /Users/adamwahab/Desktop/project-in-bioinformatics/test/lib/gtest/googletest/include -isystem /Users/adamwahab/Desktop/project-in-bioinformatics/test/lib/gtest/googletest
OBJECT_DIR = test/CMakeFiles/test_run.dir
OBJECT_FILE_DIR = test/CMakeFiles/test_run.dir/basic_tests
- TARGET_COMPILE_PDB = test/CMakeFiles/test_run.dir/
- TARGET_PDB = test/test_run.pdb
# =============================================================================
@@ -580,9 +590,8 @@ build test/test_run: CXX_EXECUTABLE_LINKER__test_run_Release test/CMakeFiles/tes
OBJECT_DIR = test/CMakeFiles/test_run.dir
POST_BUILD = cd /Users/adamwahab/Desktop/project-in-bioinformatics/cmake-build-release/test && /Applications/CLion.app/Contents/bin/cmake/mac/aarch64/bin/cmake -E make_directory /Users/adamwahab/Desktop/project-in-bioinformatics/cmake-build-release/test/test_files && /Applications/CLion.app/Contents/bin/cmake/mac/aarch64/bin/cmake -E copy_directory /Users/adamwahab/Desktop/project-in-bioinformatics/test/basic_tests/test_files /Users/adamwahab/Desktop/project-in-bioinformatics/cmake-build-release/test/test_files
PRE_LINK = :
- TARGET_COMPILE_PDB = test/CMakeFiles/test_run.dir/
TARGET_FILE = test/test_run
- TARGET_PDB = test/test_run.pdb
+ TARGET_PDB = test_run.dbg
#############################################
@@ -763,8 +772,6 @@ build test/lib/gtest/googlemock/CMakeFiles/gmock.dir/src/gmock-all.cc.o: CXX_COM
INCLUDES = -I/Users/adamwahab/Desktop/project-in-bioinformatics/test/lib/gtest/googlemock/include -I/Users/adamwahab/Desktop/project-in-bioinformatics/test/lib/gtest/googlemock -isystem /Users/adamwahab/Desktop/project-in-bioinformatics/test/lib/gtest/googletest/include -isystem /Users/adamwahab/Desktop/project-in-bioinformatics/test/lib/gtest/googletest
OBJECT_DIR = test/lib/gtest/googlemock/CMakeFiles/gmock.dir
OBJECT_FILE_DIR = test/lib/gtest/googlemock/CMakeFiles/gmock.dir/src
- TARGET_COMPILE_PDB = lib/libgmock.pdb
- TARGET_PDB = bin/libgmock.pdb
# =============================================================================
@@ -780,9 +787,8 @@ build lib/libgmock.a: CXX_STATIC_LIBRARY_LINKER__gmock_Release test/lib/gtest/go
OBJECT_DIR = test/lib/gtest/googlemock/CMakeFiles/gmock.dir
POST_BUILD = :
PRE_LINK = :
- TARGET_COMPILE_PDB = lib/libgmock.pdb
TARGET_FILE = lib/libgmock.a
- TARGET_PDB = bin/libgmock.pdb
+ TARGET_PDB = gmock.a.dbg
# =============================================================================
# Object build statements for STATIC_LIBRARY target gmock_main
@@ -799,8 +805,6 @@ build test/lib/gtest/googlemock/CMakeFiles/gmock_main.dir/src/gmock_main.cc.o: C
INCLUDES = -isystem /Users/adamwahab/Desktop/project-in-bioinformatics/test/lib/gtest/googlemock/include -isystem /Users/adamwahab/Desktop/project-in-bioinformatics/test/lib/gtest/googlemock -isystem /Users/adamwahab/Desktop/project-in-bioinformatics/test/lib/gtest/googletest/include -isystem /Users/adamwahab/Desktop/project-in-bioinformatics/test/lib/gtest/googletest
OBJECT_DIR = test/lib/gtest/googlemock/CMakeFiles/gmock_main.dir
OBJECT_FILE_DIR = test/lib/gtest/googlemock/CMakeFiles/gmock_main.dir/src
- TARGET_COMPILE_PDB = lib/libgmock_main.pdb
- TARGET_PDB = bin/libgmock_main.pdb
# =============================================================================
@@ -816,9 +820,8 @@ build lib/libgmock_main.a: CXX_STATIC_LIBRARY_LINKER__gmock_main_Release test/li
OBJECT_DIR = test/lib/gtest/googlemock/CMakeFiles/gmock_main.dir
POST_BUILD = :
PRE_LINK = :
- TARGET_COMPILE_PDB = lib/libgmock_main.pdb
TARGET_FILE = lib/libgmock_main.a
- TARGET_PDB = bin/libgmock_main.pdb
+ TARGET_PDB = gmock_main.a.dbg
#############################################
@@ -917,8 +920,6 @@ build test/lib/gtest/googletest/CMakeFiles/gtest.dir/src/gtest-all.cc.o: CXX_COM
INCLUDES = -I/Users/adamwahab/Desktop/project-in-bioinformatics/test/lib/gtest/googletest/include -I/Users/adamwahab/Desktop/project-in-bioinformatics/test/lib/gtest/googletest
OBJECT_DIR = test/lib/gtest/googletest/CMakeFiles/gtest.dir
OBJECT_FILE_DIR = test/lib/gtest/googletest/CMakeFiles/gtest.dir/src
- TARGET_COMPILE_PDB = lib/libgtest.pdb
- TARGET_PDB = bin/libgtest.pdb
# =============================================================================
@@ -934,9 +935,8 @@ build lib/libgtest.a: CXX_STATIC_LIBRARY_LINKER__gtest_Release test/lib/gtest/go
OBJECT_DIR = test/lib/gtest/googletest/CMakeFiles/gtest.dir
POST_BUILD = :
PRE_LINK = :
- TARGET_COMPILE_PDB = lib/libgtest.pdb
TARGET_FILE = lib/libgtest.a
- TARGET_PDB = bin/libgtest.pdb
+ TARGET_PDB = gtest.a.dbg
# =============================================================================
# Object build statements for STATIC_LIBRARY target gtest_main
@@ -953,8 +953,6 @@ build test/lib/gtest/googletest/CMakeFiles/gtest_main.dir/src/gtest_main.cc.o: C
INCLUDES = -isystem /Users/adamwahab/Desktop/project-in-bioinformatics/test/lib/gtest/googletest/include -isystem /Users/adamwahab/Desktop/project-in-bioinformatics/test/lib/gtest/googletest
OBJECT_DIR = test/lib/gtest/googletest/CMakeFiles/gtest_main.dir
OBJECT_FILE_DIR = test/lib/gtest/googletest/CMakeFiles/gtest_main.dir/src
- TARGET_COMPILE_PDB = lib/libgtest_main.pdb
- TARGET_PDB = bin/libgtest_main.pdb
# =============================================================================
@@ -970,9 +968,8 @@ build lib/libgtest_main.a: CXX_STATIC_LIBRARY_LINKER__gtest_main_Release test/li
OBJECT_DIR = test/lib/gtest/googletest/CMakeFiles/gtest_main.dir
POST_BUILD = :
PRE_LINK = :
- TARGET_COMPILE_PDB = lib/libgtest_main.pdb
TARGET_FILE = lib/libgtest_main.a
- TARGET_PDB = bin/libgtest_main.pdb
+ TARGET_PDB = gtest_main.a.dbg
#############################################
@@ -1068,6 +1065,8 @@ build gtest: phony lib/libgtest.a
build gtest_main: phony lib/libgtest_main.a
+build hpmodel_json: phony src/hpmodel_json
+
build imgui: phony opengl/libimgui.a
build libHPModel.a: phony src/libHPModel.a
@@ -1112,7 +1111,7 @@ build opengl/all: phony opengl/libglad.a opengl/libimgui.a opengl/libOpenGLStuff
#############################################
# Folder: /Users/adamwahab/Desktop/project-in-bioinformatics/cmake-build-release/src
-build src/all: phony src/libHPModel.a
+build src/all: phony src/libHPModel.a src/hpmodel_json
# =============================================================================
@@ -1149,14 +1148,14 @@ build test/lib/gtest/googletest/all: phony lib/libgtest.a lib/libgtest_main.a
#############################################
# Re-run CMake if any of its inputs changed.
-build build.ninja: RERUN_CMAKE | /Applications/CLion.app/Contents/bin/cmake/mac/aarch64/share/cmake-3.29/Modules/BasicConfigVersion-AnyNewerVersion.cmake.in /Applications/CLion.app/Contents/bin/cmake/mac/aarch64/share/cmake-3.29/Modules/CMakeCCompiler.cmake.in /Applications/CLion.app/Contents/bin/cmake/mac/aarch64/share/cmake-3.29/Modules/CMakeCCompilerABI.c /Applications/CLion.app/Contents/bin/cmake/mac/aarch64/share/cmake-3.29/Modules/CMakeCInformation.cmake /Applications/CLion.app/Contents/bin/cmake/mac/aarch64/share/cmake-3.29/Modules/CMakeCXXCompiler.cmake.in /Applications/CLion.app/Contents/bin/cmake/mac/aarch64/share/cmake-3.29/Modules/CMakeCXXCompilerABI.cpp /Applications/CLion.app/Contents/bin/cmake/mac/aarch64/share/cmake-3.29/Modules/CMakeCXXInformation.cmake /Applications/CLion.app/Contents/bin/cmake/mac/aarch64/share/cmake-3.29/Modules/CMakeCommonLanguageInclude.cmake /Applications/CLion.app/Contents/bin/cmake/mac/aarch64/share/cmake-3.29/Modules/CMakeCompilerIdDetection.cmake /Applications/CLion.app/Contents/bin/cmake/mac/aarch64/share/cmake-3.29/Modules/CMakeDependentOption.cmake /Applications/CLion.app/Contents/bin/cmake/mac/aarch64/share/cmake-3.29/Modules/CMakeDetermineCCompiler.cmake /Applications/CLion.app/Contents/bin/cmake/mac/aarch64/share/cmake-3.29/Modules/CMakeDetermineCXXCompiler.cmake /Applications/CLion.app/Contents/bin/cmake/mac/aarch64/share/cmake-3.29/Modules/CMakeDetermineCompileFeatures.cmake /Applications/CLion.app/Contents/bin/cmake/mac/aarch64/share/cmake-3.29/Modules/CMakeDetermineCompiler.cmake /Applications/CLion.app/Contents/bin/cmake/mac/aarch64/share/cmake-3.29/Modules/CMakeDetermineCompilerABI.cmake /Applications/CLion.app/Contents/bin/cmake/mac/aarch64/share/cmake-3.29/Modules/CMakeDetermineCompilerId.cmake /Applications/CLion.app/Contents/bin/cmake/mac/aarch64/share/cmake-3.29/Modules/CMakeDetermineSystem.cmake 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diff --git a/cmake-build-release/main_run b/cmake-build-release/main_run
new file mode 100755
index 0000000000000000000000000000000000000000..e54a49d947ef8c9fa127871f9edf69a1f12ac02a
Binary files /dev/null and b/cmake-build-release/main_run differ
diff --git a/cmake-build-release/opengl/opengl_example_run b/cmake-build-release/opengl/opengl_example_run
new file mode 100755
index 0000000000000000000000000000000000000000..6b431a334582b3163b101214121c34ac11b332dc
Binary files /dev/null and b/cmake-build-release/opengl/opengl_example_run differ
diff --git a/cmake-build-release/src/hpmodel_json b/cmake-build-release/src/hpmodel_json
new file mode 100755
index 0000000000000000000000000000000000000000..8a35a3d4ecb3766218285ed737053f44a96f0753
Binary files /dev/null and b/cmake-build-release/src/hpmodel_json differ
diff --git a/cmake-build-release/test/test_files/points_no_hydrophobes.json b/cmake-build-release/test/test_files/points_no_hydrophobes.json
new file mode 100644
index 0000000000000000000000000000000000000000..32acbc0816a471ee73578ae543e0fde17a500737
--- /dev/null
+++ b/cmake-build-release/test/test_files/points_no_hydrophobes.json
@@ -0,0 +1,32 @@
+[
+ {
+ "x": 0,
+ "y": 0,
+ "z": 0,
+ "hydrophobic": false
+ },
+ {
+ "x": 1,
+ "y": 0,
+ "z": 0,
+ "hydrophobic": false
+ },
+ {
+ "x": 1,
+ "y": 1,
+ "z": 0,
+ "hydrophobic": false
+ },
+ {
+ "x": 0,
+ "y": 1,
+ "z": 0,
+ "hydrophobic": false
+ },
+ {
+ "x": 0,
+ "y": 1,
+ "z": -1,
+ "hydrophobic": false
+ }
+]
\ No newline at end of file
diff --git a/cmake-build-release/test/test_files/points_with_hydrophobes.json b/cmake-build-release/test/test_files/points_with_hydrophobes.json
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/cmake-build-release/test/test_run b/cmake-build-release/test/test_run
new file mode 100755
index 0000000000000000000000000000000000000000..88338008e30a80c23643d2736535c5472a153dd7
Binary files /dev/null and b/cmake-build-release/test/test_run differ
diff --git a/opengl/opengl_visualization.cpp b/opengl/opengl_visualization.cpp
index 9a047e7858384377d5a6dd26abf55de74bbb755a..a206e28718d94121b0bb5108d765b457b1325c4d 100644
--- a/opengl/opengl_visualization.cpp
+++ b/opengl/opengl_visualization.cpp
@@ -15,6 +15,7 @@
#include <iostream>
#include <vector>
#include <map>
+#include <sstream>
#include <tuple>
#include <string>
@@ -55,6 +56,10 @@ int lineThicknessInt = 3; // Default line thickness
float sphereScale = 1.0f; // Scaling factor for sphere size
float lineThickness = 3.0f; // Line thickness
+// New global variables for JSON input
+char jsonInput[1024 * 16] = "";
+std::string jsonErrorMessage = "";
+
// Function prototypes
void framebuffer_size_callback(GLFWwindow* window, int width, int height);
void processInput(GLFWwindow *window);
@@ -84,6 +89,9 @@ void updateWindowTitle(GLFWwindow* window, bool showUI);
// Helper function to convert world coordinates to screen coordinates
bool WorldToScreen(const glm::vec3& worldPos, const glm::mat4& view, const glm::mat4& projection, ImVec2& screenPos);
+// Function to parse JSON input
+bool parseHPModelJson(const std::string& jsonInput, std::map<std::tuple<int, int, int>, Sphere>& spheres, std::string& errorMessage);
+
// Entry point
int main()
{
@@ -384,7 +392,6 @@ int main()
updateLines(spheres, lineVertices, lineVBO);
}
- // New GUI options
ImGui::Checkbox("Show Grid Points", &showGridPoints);
ImGui::InputInt("Sphere Size", &sphereSizeInt);
@@ -397,6 +404,31 @@ int main()
if (lineThicknessInt > 10) lineThicknessInt = 10;
lineThickness = static_cast<float>(lineThicknessInt);
+ // Add JSON input field
+ ImGui::Text("JSON Input:");
+ ImGui::InputTextMultiline("##jsonInput", jsonInput, sizeof(jsonInput), ImVec2(-1.0f, 150.0f));
+
+ if (ImGui::Button("Submit JSON"))
+ {
+ std::string jsonErrorMessage = "";
+ std::string jsonString(jsonInput); // Convert char[] to std::string
+ if (parseHPModelJson(jsonInput, spheres, jsonErrorMessage))
+ {
+ // Update lines connecting the spheres
+ updateLines(spheres, lineVertices, lineVBO);
+ }
+ else
+ {
+ // Parsing failed, error message is set
+ }
+ }
+
+ // Display error message if parsing failed
+ if (!jsonErrorMessage.empty())
+ {
+ ImGui::TextColored(ImVec4(1.0f, 0.0f, 0.0f, 1.0f), "%s", jsonErrorMessage.c_str());
+ }
+
ImGui::End();
}
@@ -474,7 +506,7 @@ int main()
{
glm::mat4 model = glm::mat4(1.0f);
model = glm::translate(model, sphere.position);
- model = glm::scale(model, glm::vec3(sphereScale)); // Apply scaling
+ model = glm::scale(model, glm::vec3(sphereScale)); // Scale each sphere
glUniformMatrix4fv(modelLoc, 1, GL_FALSE, glm::value_ptr(model));
@@ -814,4 +846,183 @@ bool WorldToScreen(const glm::vec3& worldPos, const glm::mat4& view, const glm::
screenPos = ImVec2(windowX, windowY);
return true;
-}
\ No newline at end of file
+}
+
+bool parseHPModelJson(const std::string& jsonInput, std::map<std::tuple<int, int, int>, Sphere>& spheres, std::string& errorMessage)
+{
+ // Remove all whitespace
+ std::string input;
+ for (char c : jsonInput)
+ {
+ if (!isspace(static_cast<unsigned char>(c)))
+ input += c;
+ }
+
+ if (input.empty())
+ {
+ errorMessage = "Input is empty.";
+ return false;
+ }
+
+ if (input.front() != '[' || input.back() != ']')
+ {
+ errorMessage = "JSON must start with '[' and end with ']'.";
+ return false;
+ }
+
+ input = input.substr(1, input.size() - 2); // Remove '[' and ']'
+
+ size_t pos = 0;
+ while (pos < input.size())
+ {
+ if (input[pos] != '{')
+ {
+ errorMessage = "Expected '{' at position " + std::to_string(pos);
+ return false;
+ }
+
+ size_t endPos = input.find('}', pos);
+ if (endPos == std::string::npos)
+ {
+ errorMessage = "Expected '}' after position " + std::to_string(pos);
+ return false;
+ }
+
+ std::string objStr = input.substr(pos + 1, endPos - pos - 1); // Get content inside '{' and '}'
+
+ // Parse the object string
+ int x = 0, y = 0, z = 0;
+ bool hydrophobic = false;
+ bool xSet = false, ySet = false, zSet = false, hydroSet = false;
+
+ size_t objPos = 0;
+ while (objPos < objStr.size())
+ {
+ // Find key
+ if (objStr[objPos] != '"')
+ {
+ errorMessage = "Expected '\"' for key at position " + std::to_string(objPos);
+ return false;
+ }
+ size_t keyEnd = objStr.find('"', objPos + 1);
+ if (keyEnd == std::string::npos)
+ {
+ errorMessage = "Expected '\"' to end key at position " + std::to_string(objPos + 1);
+ return false;
+ }
+
+ std::string key = objStr.substr(objPos + 1, keyEnd - objPos - 1);
+
+ // Find ':'
+ size_t colonPos = objStr.find(':', keyEnd + 1);
+ if (colonPos == std::string::npos)
+ {
+ errorMessage = "Expected ':' after key \"" + key + "\"";
+ return false;
+ }
+
+ // Find value
+ size_t valueStart = colonPos + 1;
+ size_t valueEnd = valueStart;
+
+ if (key == "hydrophobic")
+ {
+ // Value should be 'true' or 'false'
+ if (objStr.compare(valueStart, 4, "true") == 0)
+ {
+ hydrophobic = true;
+ valueEnd = valueStart + 4;
+ }
+ else if (objStr.compare(valueStart, 5, "false") == 0)
+ {
+ hydrophobic = false;
+ valueEnd = valueStart + 5;
+ }
+ else
+ {
+ errorMessage = "Invalid value for key \"hydrophobic\"";
+ return false;
+ }
+ hydroSet = true;
+ }
+ else
+ {
+ // Value should be an integer
+ size_t numEnd = valueStart;
+ if (objStr[numEnd] == '-') numEnd++; // Handle negative numbers
+ while (numEnd < objStr.size() && isdigit(objStr[numEnd]))
+ {
+ numEnd++;
+ }
+ if (numEnd == valueStart)
+ {
+ errorMessage = "Invalid integer value for key \"" + key + "\"";
+ return false;
+ }
+ std::string valueStr = objStr.substr(valueStart, numEnd - valueStart);
+ int value = 0;
+ try
+ {
+ value = std::stoi(valueStr);
+ }
+ catch (std::exception&)
+ {
+ errorMessage = "Invalid integer value for key \"" + key + "\"";
+ return false;
+ }
+ if (key == "x")
+ {
+ x = value;
+ xSet = true;
+ }
+ else if (key == "y")
+ {
+ y = value;
+ ySet = true;
+ }
+ else if (key == "z")
+ {
+ z = value;
+ zSet = true;
+ }
+ else
+ {
+ errorMessage = "Unexpected key \"" + key + "\"";
+ return false;
+ }
+ valueEnd = numEnd;
+ }
+
+ // Skip commas
+ objPos = valueEnd;
+ if (objPos < objStr.size() && objStr[objPos] == ',')
+ {
+ objPos++;
+ }
+ }
+
+ if (!xSet || !ySet || !zSet || !hydroSet)
+ {
+ errorMessage = "Missing key(s) in object.";
+ return false;
+ }
+
+ // Add sphere
+ Sphere sphere;
+ sphere.position = glm::vec3(x, y, -z); // Adjust Z-axis as in your code
+ sphere.color = hydrophobic ? glm::vec3(1.0f, 0.0f, 0.0f) : glm::vec3(0.5f, 0.5f, 0.5f);
+
+ spheres[std::make_tuple(x, y, z)] = sphere;
+
+ // Move pos to after the '}'
+ pos = endPos + 1;
+
+ // Skip commas
+ if (pos < input.size() && input[pos] == ',')
+ {
+ pos++;
+ }
+ }
+
+ return true;
+}
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index 6a3a376e0aef96c1b192988e157c01ff2d7f8cab..4492e6db7b16f38e2b40084ddadf96528f0d336a 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -1,5 +1,9 @@
-set(SOURCE_FILES HPModel.cpp)
+set(SOURCE_FILES HPModel.cpp
+ hpmodel_json.cpp)
add_library(HPModel STATIC ${SOURCE_FILES})
target_include_directories(HPModel PUBLIC ${CMAKE_CURRENT_SOURCE_DIR} fmt)
+
+add_executable(hpmodel_json hpmodel_json.cpp)
+target_link_libraries(hpmodel_json HPModel)
diff --git a/src/hpmodel_json.cpp b/src/hpmodel_json.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..6a3ae65906f7f4ab4678adbead3ab047d1f35fa0
--- /dev/null
+++ b/src/hpmodel_json.cpp
@@ -0,0 +1,43 @@
+// hpmodel_json.cpp
+
+#include "HPModel.h"
+#include <iostream>
+#include <fstream>
+
+int main()
+{
+ // Create an HPModel instance with a given sequence
+ std::string sequence = "pppp";
+ HPModel model(sequence);
+
+ try
+ {
+ model.fold(UP);
+ model.fold(UP);
+ model.fold(UP);
+ }
+ catch (const std::exception& e)
+ {
+ std::cerr << "Error folding model: " << e.what() << std::endl;
+ return 1;
+ }
+
+ // Serialize points to JSON
+ std::string jsonOutput = model.pointsToJson();
+
+ // Write JSON to file
+ std::ofstream outFile("hpmodel_output.json");
+ if (outFile.is_open())
+ {
+ outFile << jsonOutput;
+ outFile.close();
+ std::cout << "JSON data written to hpmodel_output.json" << std::endl;
+ }
+ else
+ {
+ std::cerr << "Failed to write JSON data to file" << std::endl;
+ return 1;
+ }
+
+ return 0;
+}
\ No newline at end of file
diff --git a/src/hpmodel_json.h b/src/hpmodel_json.h
new file mode 100644
index 0000000000000000000000000000000000000000..ae2d383066b10fcebddb0835e7590efdda041aa7
--- /dev/null
+++ b/src/hpmodel_json.h
@@ -0,0 +1,82 @@
+// HPModel.h
+
+#ifndef HPMODEL_H
+#define HPMODEL_H
+
+#include <iostream>
+#include <vector>
+#include <string>
+#include <stdexcept>
+
+// Enum for relative direction of folding
+enum DIRECTION {
+ FORWARD,
+ UP,
+ DOWN,
+ LEFT,
+ RIGHT
+};
+
+// Enum for absolute direction in 3D space
+enum ABSOLUTE_DIRECTION {
+ NORTH,
+ EAST,
+ SOUTH,
+ WEST,
+ ABS_UP,
+ ABS_DOWN
+};
+
+// Enum for rotation state
+enum ROTATION {
+ NO_ROTATION,
+ ROTATE_90,
+ ROTATE_180,
+ ROTATE_270
+};
+
+// Class representing a point in 3D space
+class Point {
+public:
+ int x;
+ int y;
+ int z;
+ bool hydrophobic;
+
+ Point(const int x, const int y, const int z, const bool hydrophobic);
+ void print() const;
+ bool coords_match(Point other) const;
+};
+
+// HPModel class representing the HP protein folding model
+class HPModel {
+private:
+ std::vector<Point> acids; // The list of amino acids in the chain
+ std::string sequence; // The HP sequence (e.g., "hphph")
+
+ ABSOLUTE_DIRECTION currentDirection;
+ ABSOLUTE_DIRECTION previousDirection;
+ ROTATION rotation;
+
+ void updateCurrentDirection(DIRECTION direction);
+ ABSOLUTE_DIRECTION getPlaneDirectionChange(ABSOLUTE_DIRECTION absolute_direction, DIRECTION relative_direction);
+ ABSOLUTE_DIRECTION getUpDownDirectionAndUpdatePrevious(DIRECTION relative_direction);
+ bool isInsertValid(Point toInsert);
+ Point getHead();
+ bool isCurrentAcidHydrophobic();
+ void addPoint(DIRECTION direction, bool isHydrophobic);
+ DIRECTION getRotatedRelativeDirection(DIRECTION relative_direction);
+ ABSOLUTE_DIRECTION invertDirection(ABSOLUTE_DIRECTION direction);
+ void rotate(int amount);
+
+public:
+ HPModel(const std::string &input_sequence);
+
+ void fold(DIRECTION direction);
+ void print() const;
+ std::vector<Point> getPoints();
+ std::string pointsToJson() const;
+ static std::string directionToString(DIRECTION direction);
+};
+
+#endif // HPMODEL_H
\ No newline at end of file